Step 1
Preheat oven to 375 degrees F (190 degrees C). Spray a baking sheet and a 9-inch square baking dish with cooking spray.
Step 2
Pierce the squash halves with a fork and arrange cut-side down on the prepared baking sheet.
Step 3
Bake squash in the preheated oven until a knife easily slices into the flesh about 1 hour 20 minutes. Remove squash from oven and cool until cool enough to handle at least 15 minutes.
Step 4
Place bacon in a large skillet or Dutch oven; cook and stir over medium-high heat until evenly browned about 10 minutes. Remove bacon with a slotted spoon and drain on a paper towel-lined plate reserving about 1 tablespoon drippings in the skillet. If the drippings don't equal 1 tablespoon add olive oil to the skillet and heat over medium heat.
Step 5
Cook and stir onion and garlic in the bacon drippings over medium heat until golden brown 10 to 15 minutes; season with salt.
Step 6
Slowly pour wine over the onion mixture and bring to a boil while scraping the browned bits of food off of the bottom of the skillet with a wooden spoon; add tomatoes and Italian seasoning Season tomato mixture with black pepper. Cook and stir tomato mixture over medium-high heat until sauce is thickened about 5 minutes.
Step 7
Shred the spaghetti squash meat using a fork discarding the peel. Stir squash meat into tomato sauce until evenly incorporated; spoon into the prepared baking dish. Sprinkle mozzarella cheese and Parmesan cheese over squash mixture.
Step 8
Bake in the preheated oven until cheese is melted and browned 20 to 30 minutes. Top cheese layer with bacon.